In one of a handful of autobiographical sketches Cotton explained he was recruited in New York by the wife of Thomas Maguire, the San Francisco theatre magnate. His route West meant crossing Panama on the railroad, beginning on the Gulf of Mexico at Aspinwall (subsequently Colon), and departing from the Pacific side on the Steamship Golden Gate. Once in San Francisco he was immediately on Maguire's stage. This was a point in time (1862) when California's role in the national conflict was yet to be determined. By year's end he had two brothers and a brother-in-law in the Union army. Several patriotic songs he sung became local hits: "Our Union Right or Wrong," and "Abraham's Daughter." The latter was written by Septimus Weiner. It was a remarkable period of time for Cotton. His first songsters were published, as well as his first sheetmusic. Maguire's house band - the San Francisco Minstrels (Cotton, Birch, Wambold, & Backus) - went traveling through the inland mining regions on the nascent circuit of theatres owned by the impresario.
Working for Maguire was a big break. Their relationship was a long one, with significant highs and lows. When Cotton left San Francisco three years later, in 1864, it was in the wake of a court injunction prohibiting him from performing.